Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to those that can be cultured in the lab. But it excluded a huge portion of the microbiome that could not survive on lab conditions. In the past few years, the culture-independent metagenomic sequencing enabled us to explore the complex microbial community coexisting within and on us. Metagenomics has equipped us with new avenues of investigating the microbiome, from studying a single species to a complex community in a dynamic ecosystem. Thus, identifying the involved microbes and their genomes becomes one of the core tasks in metagenomic sequencing. Metagenome-assembled genomes are groups of contigs with similar sequence characteristics from de novo assembly and could represent the microbial genomes from metagenomic sequencing. In this paper, we reviewed a spectrum of tools for producing and annotating metagenome-assembled genomes from metagenomic sequencing data and discussed their technical and biological perspectives.
To accelerate the solution of large eigenvalue problems arising from many-body calculations in nuclear physics on distributed-memory parallel systems equipped with general-purpose Graphic Processing Units (GPUs), we modified a previously developed hybrid MPI/OpenMP implementation of an eigensolver written in FORTRAN 90 by using an OpenACC directives based programming model. Such an approach requires making minimal changes to the original code and enables a smooth migration of large-scale nuclear structure simulations from a distributed-memory many-core CPU system to a distributed GPU system. However, in order to make the OpenACC based eigensolver run efficiently on GPUs, we need to take into account the architectural differences between a many-core CPU and a GPU device. Consequently, the optimal way to insert OpenACC directives may be different from the original way of inserting OpenMP directives. We point out these differences in the implementation of sparse matrix-matrix multiplications (SpMM), which constitutes the main cost of the eigensolver, as well as other differences in the preconditioning step and dense linear algebra operations. We compare the performance of the OpenACC based implementation executed on multiple GPUs with the performance on distributed-memory many-core CPUs, and demonstrate significant speedup achieved on GPUs compared to the on-node performance of a many-core CPU. We also show that the overall performance improvement of the eigensolver on multiple GPUs is more modest due to the communication overhead among different MPI ranks.
We describe an unsupervised domain adaptation method for image content shift caused by viewpoint changes for a semantic segmentation task. Most existing methods perform domain alignment in a shared space and assume that the mapping from the aligned space to the output is transferable. However, the novel content induced by viewpoint changes may nullify such a space for effective alignments, thus resulting in negative adaptation. Our method works without aligning any statistics of the images between the two domains. Instead, it utilizes a view transformation network trained only on color images to hallucinate the semantic images for the target. Despite the lack of supervision, the view transformation network can still generalize to semantic images thanks to the inductive bias introduced by the attention mechanism. Furthermore, to resolve ambiguities in converting the semantic images to semantic labels, we treat the view transformation network as a functional representation of an unknown mapping implied by the color images and propose functional label hallucination to generate pseudo-labels in the target domain. Our method surpasses baselines built on state-of-the-art correspondence estimation and view synthesis methods. Moreover, it outperforms the state-of-the-art unsupervised domain adaptation methods that utilize self-training and adversarial domain alignment. Our code and dataset will be made publicly available.
We describe a method for realistic depth synthesis that learns diverse variations from the real depth scans and ensures geometric consistency for effective synthetic-to-real transfer. Unlike general image synthesis pipelines, where geometries are mostly ignored, we treat geometries carried by the depth based on their own existence. We propose differential contrastive learning that explicitly enforces the underlying geometric properties to be invariant regarding the real variations been learned. The resulting depth synthesis method is task-agnostic and can be used for training any task-specific networks with synthetic labels. We demonstrate the effectiveness of the proposed method by extensive evaluations on downstream real-world geometric reasoning tasks. We show our method achieves better synthetic-to-real transfer performance than the other state-of-the-art. When fine-tuned on a small number of real-world annotations, our method can even surpass the fully supervised baselines.
With the increasing demand for search and rescue, it is highly demanded to detect objects of interest in large-scale images captured by Unmanned Aerial Vehicles (UAVs), which is quite challenging due to extremely small scales of objects. Most existing methods employed Feature Pyramid Network (FPN) to enrich shallow layers features by combing deep layers contextual features. However, under the limitation of the inconsistency in gradient computation across different layers, the shallow layers in FPN are not fully exploited to detect tiny objects. In this paper, we propose a Scale Selection Pyramid network (SSPNet) for tiny person detection, which consists of three components: Context Attention Module (CAM), Scale Enhancement Module (SEM), and Scale Selection Module (SSM). CAM takes account of context information to produce hierarchical attention heatmaps. SEM highlights features of specific scales at different layers, leading the detector to focus on objects of specific scales instead of vast backgrounds. SSM exploits adjacent layers relationships to fulfill suitable feature sharing between deep layers and shallow layers, thereby avoiding the inconsistency in gradient computation across different layers. Besides, we propose a Weighted Negative Sampling (WNS) strategy to guide the detector to select more representative samples. Experiments on the TinyPerson benchmark show that our method outperforms other state-of-the-art (SOTA) detectors.
The 1-2-3 Conjecture, posed by Karo{n}ski, {L}uczak and Thomason, asked whether every connected graph $G$ different from $K_2$ can be 3-edge-weighted so that every two adjacent vertices of $G$ get distinct sums of incident weights. The 1-2 Conjecture states that if vertices also receive colors and the vertex color is added to the sum of its incident edges, then adjacent vertices can be distinguished using only ${ 1,2}$. In this paper we confirm 1-2 Conjecture for 3-regular graphs. Meanwhile, we show that every 3-regular graph can achieve a neighbor sum distinguishing edge coloring by using 4 colors, which answers 1-2-3 Conjecture positively.
Neural text generation models are typically trained by maximizing log-likelihood with the sequence cross entropy loss, which encourages an exact token-by-token match between a target sequence with a generated sequence. Such training objective is sub-optimal when the target sequence not perfect, e.g., when the target sequence is corrupted with noises, or when only weak sequence supervision is available. To address this challenge, we propose a novel Edit-Invariant Sequence Loss (EISL), which computes the matching loss of a target n-gram with all n-grams in the generated sequence. EISL draws inspirations from convolutional networks (ConvNets) which are shift-invariant to images, hence is robust to the shift of n-grams to tolerate edits in the target sequences. Moreover, the computation of EISL is essentially a convolution operation with target n-grams as kernels, which is easy to implement with existing libraries. To demonstrate the effectiveness of EISL, we conduct experiments on three tasks: machine translation with noisy target sequences, unsupervised text style transfer, and non-autoregressive machine translation. Experimental results show our method significantly outperforms cross entropy loss on these three tasks.
Unsupervised domain adaptation (UDA) aims to transfer knowledge learned from a labeled source domain to an unlabeled and unseen target domain, which is usually trained on data from both domains. Access to the source domain data at the adaptation stage, however, is often limited, due to data storage or privacy issues. To alleviate this, in this work, we target source free UDA for segmentation, and propose to adapt an ``off-the-shelf segmentation model pre-trained in the source domain to the target domain, with an adaptive batch-wise normalization statistics adaptation framework. Specifically, the domain-specific low-order batch statistics, i.e., mean and variance, are gradually adapted with an exponential momentum decay scheme, while the consistency of domain shareable high-order batch statistics, i.e., scaling and shifting parameters, is explicitly enforced by our optimization objective. The transferability of each channel is adaptively measured first from which to balance the contribution of each channel. Moreover, the proposed source free UDA framework is orthogonal to unsupervised learning methods, e.g., self-entropy minimization, which can thus be simply added on top of our framework. Extensive experiments on the BraTS 2018 database show that our source free UDA framework outperformed existing source-relaxed UDA methods for the cross-subtype UDA segmentation task and yielded comparable results for the cross-modality UDA segmentation task, compared with a supervised UDA methods with the source data.
The unified streaming and non-streaming two-pass (U2) end-to-end model for speech recognition has shown great performance in terms of streaming capability, accuracy, real-time factor (RTF), and latency. In this paper, we present U2++, an enhanced version of U2 to further improve the accuracy. The core idea of U2++ is to use the forward and the backward information of the labeling sequences at the same time at training to learn richer information, and combine the forward and backward prediction at decoding to give more accurate recognition results. We also proposed a new data augmentation method called SpecSub to help the U2++ model to be more accurate and robust. Our experiments show that, compared with U2, U2++ shows faster convergence at training, better robustness to the decoding method, as well as consistent 5% - 8% word error rate reduction gain over U2. On the experiment of AISHELL-1, we achieve a 4.63% character error rate (CER) with a non-streaming setup and 5.05% with a streaming setup with 320ms latency by U2++. To the best of our knowledge, 5.05% is the best-published streaming result on the AISHELL-1 test set.
The existing human pose estimation methods are confronted with inaccurate long-distance regression or high computational cost due to the complex learning objectives. This work proposes a novel deep learning framework for human pose estimation called composite localization to divide the complex learning objective into two simpler ones: a sparse heatmap to find the keypoints approximate location and two short-distance offsetmaps to obtain its final precise coordinates. To realize the framework, we construct two types of composite localization networks: CLNet-ResNet and CLNet-Hourglass. We evaluate the networks on three benchmark datasets, including the Leeds Sports Pose dataset, the MPII Human Pose dataset, and the COCO keypoints detection dataset. The experimental results show that our CLNet-ResNet50 outperforms SimpleBaseline by 1.14% with about 1/2 GFLOPs. Our CLNet-Hourglass outperforms the original stacked-hourglass by 4.45% on COCO.
